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Journal of Virology, October 2000, p. 9601-9609, Vol. 74, No. 20
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Attenuation of Tick-Borne Encephalitis Virus by
Structure-Based Site-Specific Mutagenesis of a Putative
Flavivirus Receptor Binding Site
Christian W.
Mandl,*
Steven L.
Allison,
Heidemarie
Holzmann,
Tamara
Meixner, and
Franz X.
Heinz
Institute of Virology, University of Vienna, A-1095
Vienna, Austria
Received 6 April 2000/Accepted 10 July 2000
 |
ABSTRACT |
The impact of a specific region of the envelope protein E of
tick-borne encephalitis (TBE) virus on the biology of this virus was
investigated by a site-directed mutagenesis approach. The four amino
acid residues that were analyzed in detail (E308 to E311) are located
on the upper-lateral surface of domain III according to the X-ray
structure of the TBE virus protein E and are part of an area that is
considered to be a potential receptor binding determinant of
flaviviruses. Mutants containing single amino acid substitutions, as
well as combinations of mutations, were constructed and analyzed for
their virulence in mice, growth properties in cultured cells, and
genetic stability. The most significant attenuation in mice was
achieved by mutagenesis of threonine 310. Combining this mutation with
deletion mutations in the 3'-noncoding region yielded mutants that were
highly attenuated. The biological effects of mutation Thr 310 to Lys,
however, could be reversed to a large degree by a mutation at a
neighboring position (Lys 311 to Glu) that arose spontaneously during
infection of a mouse. Mutagenesis of the other positions provided
evidence for the functional importance of residue 308 (Asp) and its
charge interaction with residue 311 (Lys), whereas residue 309 could be
altered or even deleted without any notable consequences. Deletion of
residue 309 was accompanied by a spontaneous second-site mutation (Phe
to Tyr) at position 332, which in the three-dimensional structure of
protein E is spatially close to residue 309. The information obtained
in this study is relevant for the development of specific attenuated
flavivirus strains that may serve as future live vaccines.
 |
INTRODUCTION |
Tick-borne encephalitis
(TBE) virus is a human pathogenic member of the genus
Flavivirus (family Flaviviridae) (31).
Many members of this genus can cause severe human diseases, the most important representatives besides TBE virus being the mosquito-borne viruses yellow fever (YF) virus, Japanese encephalitis (JE) virus, and
the four serotypes of dengue virus (18). In spite of the availability of attenuated live vaccines (in the case of YF virus) and
formalin-inactivated killed vaccines (TBE virus, JE virus) which have
proven to be effective for the prevention of flavivirus infections,
there is a strong demand for the development of novel and improved
vaccines against these and other flavivirus infections. For the
rational design of live vaccines, a detailed understanding of the
molecular basis of virulence and pathogenesis is a major goal. With the
availability of modern molecular techniques and high-resolution
structural information, it is now possible to alter viral structures in
a specific and rational way in order to understand structure-function
relationships. This knowledge can then be applied to achieve the
desired biological property, such as attenuation of the virus.
Flavivirus virions are relatively simple particles consisting of a
nucleocapsid composed of a single capsid protein (C) surrounded by a
lipid membrane that contains two viral proteins, the small membrane
protein M and the large envelope glycoprotein E (23). The
nucleocapsid contains the viral genome, an unsegmented
positive-stranded RNA of approximately 11 kb that is capped at the 5'
end but exhibits an elaborate RNA secondary structure rather than a
poly(A) tail at its 3' end (20). This RNA, which
simultaneously serves as the only viral messenger, encodes all of the
viral proteins (the three structural proteins C, M, and E and seven
nonstructural proteins) in a single long open reading frame. The
construction of infectious cDNA clones for a growing number of
flaviviruses, including TBE virus (24), during the past 10 years has made it possible to specifically mutate flaviviruses and
study the effects of individual mutations on the biology of these
viruses. For instance, certain deletions engineered into the
3'-noncoding region (NCR) of TBE virus have been shown to produce
strong attenuation of this virus in the mouse model (16).
The envelope protein E appears to be particularly important for
virulence, since it is responsible for some of the most crucial functions during the flavivirus life cycle: it mediates primary attachment of the virus to its target cell and thus determines, at
least in part, the host-cell tropism and pathogenesis of the virus.
After attachment and uptake of the virus by endocytosis, protein E is
triggered by an acid-induced conformational change to mediate fusion of
the viral and cellular membranes enabling the nucleocapsid to be
released into the cytoplasm. Protein E is also the major target of
neutralizing antibodies produced by the host and by itself is
sufficient to elicit a protective immune response. The solution of the
atomic structure of the ectodomain of protein E of TBE virus by X-ray
crystallography (22) revealed that this protein does not
form protruding spikes that are perpendicular to the viral surface but
instead is arranged as a head-to-tail homodimer that is oriented
parallel to the viral membrane. Each monomer consists of three
structurally distinct domains, referred to as domain I (central
domain), domain II (dimerization domain), and domain III, which
exhibits the characteristic fold of an immunoglobulin constant domain.
Analysis of mutants of different flaviviruses with altered virulence
properties including tissue-culture-adapted mutants, neutralization
escape mutants, naturally occurring virus variants, vaccine strains
and, most recently, mutants generated by site-specific mutagenesis
reviewed in reference (17) has revealed numerous mutations
within protein E that influence virulence and pathogenesis. Interestingly, mapping of these mutations on the molecular structure of
protein E indicated that they formed three distinct clusters (22). First, there are mutations at or near the tip of
domain II, which is believed to contain the fusion peptide. Another
cluster is located within a predicted hinge region connecting domains I
and II, which is probably involved in the acid-induced conformational change. Thus, the mutations of these two clusters are likely to affect
virulence by influencing fusion activity. The third cluster is on the
upper and distal-lateral surface of domain III, which has been proposed
to be involved in receptor binding, and this may be the functional
basis of how these mutations influence the virulence of flaviviruses.
Aside from dengue type 2 virus, for which a requirement for heparan
sulfate binding has been demonstrated (2), no specific
flavivirus cellular receptors have been definitively identified, but
some reports indicate the presence of various cell surface proteins
with specific binding affinities for different flaviviruses (10,
11, 19, 27). An involvement of the lateral surface of domain III
in cell attachment is suggested by several lines of indirect evidence
(12, 22), including the immunoglobulin-like fold of this
domain, which is characteristically found in many proteins with
specific binding functions, the high density of charged surface
residues on the lateral surface, the presence of an RGD motif in some
mosquito-borne flaviviruses (which is known in other cases to be
recognized by members of the integrin protein familiy), and the
identification of mutations in this region in host range mutants
(14) and mutants with altered virulence properties (1,
3, 4, 8, 9, 13, 26).
In this study we introduced mutations at four positions (residues 308 to 311) of the upper-lateral surface of domain III of the TBE virus
protein E and investigated their influence on biological properties of
the resulting mutant viruses. For each position distinct effects on the
genetic stability, growth properties in cell culture, and virulence in
mice were observed. Most importantly, a substitution of position 310 from Thr to Lys resulted in significant attenuation, which could be
further enhanced by combining this mutation with previously described
deletion mutations in the 3'-NCR.
 |
MATERIALS AND METHODS |
Virus and infectious cDNA clone.
All mutants were derived
from prototype strain Neudoerfl of Western subtype TBE virus, which was
also used as the wild-type control in all experiments. The biological
properties of this virus, including virulence, have been previously
characterized in detail (16), and its complete genomic
sequence is known (GenBank accession no. U27495). Specific mutants of
this virus strain were engineered using previously described cDNA
clones from which infectious RNA was transcribed in vitro
(15). Plasmid pTNd/c contains cDNA corresponding to the
entire genome of TBE virus strain Neudoerfl. Plasmids pTNd/5' and
pTNd/3' contain cDNAs corresponding to the 5' one-third and the 3'
two-thirds of the genome, respectively, and after in vitro ligation
infectious full-length RNA can be transcribed from these plasmids.
Plasmids pTNd/3'
10847 and pTNd/3'
10919 contain deletions within
the 3'-NCR extending from the stop codon of the single long open
reading frame to the designated position. These plasmids and the
properties of the virus mutants derived from them were described
previously (16).
Cloning procedures.
All protein E mutations were introduced
into plasmid pTNd/5' by swapping the small (110 bp) SnaBI
(at position 1878 of the TBE strain Neudoerfl genome)-BamHI
(at position 1988) fragment with a PCR-derived fragment containing the
desired mutation(s). Both SnaBI and BamHI have
unique recognition sequences within pTNd/5'. The sequences of the
mutagenic sense primers and the antisense primer which were used for
all constructs are listed in Table 1.
Virus recovery and stock virus preparations.
The mutated
derivatives of plasmid pTNd/5' and plasmid pTNd/3' or its derivatives
carrying 3'-NCR deletion mutations (16) were joined by in
vitro ligation at the unique ClaI restriction site to give
full-length templates for subsequent RNA transcription by T7 RNA
polymerase. The generation of genome-length RNA, its purification, and
its transfection into BHK 21 cells by electroporation were performed as
described elsewhere (15). Three to five days after
electroporation, cell culture supernatants were usually found to be
positive for TBE virus protein E using a four-layer enzyme-linked
immunosorbent assay (ELISA) (6). In order to achieve
sufficient amounts of high-titer virus stocks with a minimum of viral
passages, litters of suckling mice were infected intracranially with
the cell culture supernatant. Virus was then passaged a second time in
suckling-mouse brain, and 20% (wt/vol) suspensions of brain homogenate
were prepared to serve as virus stocks for all subsequent experiments.
Sequence analysis.
Sequencing was performed with an
automated DNA sequencing system (ABI-Perkin-Elmer). New plasmid
constructions were checked by sequence analysis over the entire protein
E coding region and in the vicinity of restriction sites used for
cloning. The protein E coding region of all mutant virus stocks and
from virus present in the brain of two adult mice killed by each mutant
was sequenced. For these analyses, genomic RNA was purified from
suckling mouse or adult mouse brains and analyzed by reverse
transcription-PCR (RT-PCR) by standard methods and as described
previously (29). PCR-derived fragments were sequenced
directly and on both strands.
Cell cultures.
BHK-21 cells, porcine kidney (PS) cells, and
primary chicken embryo (CE) cells were grown under standard conditions
as described previously (7, 15). Infectivity values of virus
stocks were determined by plaque titer determinations on PS cells
(7) and confirmed by endpoint dilution infection experiments
on BHK-21 and CE cells. To test for temperature sensitivity, plaque
tests were performed at the standard incubation temperature (37°C)
and at an elevated temperature (40°C), and the number and morphology of the plaques were evaluated. Growth capacities in CE cells were determined as described in detail elsewhere (15). Briefly,
cells were infected at a multiplicity of infection (MOI) of
approximately 1, and virus released from the cells within 1-h periods
was collected from the supernatant at several times postinfection. The
infectious titers of these samples were determined by standard plaque assays.
Animal model.
Virulence and infectivity characteristics were
analyzed in outbred Swiss albino mice. Groups of 10 5-week-old (body
weight, approximately 20 g) mice were inoculated subcutaneously,
and survival was recorded for 28 days. Mice were then bled, and
seroconversion was investigated by a TBE virus-antibody ELISA
(5). For the determination of the 50% lethal dose
(LD50) and the 50% infectious dose (ID50),
mice were inoculated with sequential 10-fold dilutions of virus ranging
from 1 to 105 (and 106, where appropriate) PFU.
The calculation of LD50 and ID50 values was
performed by the method of Reed and Muench (21). For
ID50 calculations, the number of infected mice was taken to
be the total of mice killed plus the surviving mice with detectable
seroconversion. Surviving mice without detectable serum antibody were
scored as uninfected. To test whether seroconverted mice had developed
a protective immunity, mice were inoculated with a challenge dose of
100 LD50 of the highly virulent TBE virus strain Hypr
(30).
Protein structure graphics.
The three-dimensional structure
of a soluble ectodomain fragment of the TBE virus envelope protein at
2.0 Å resolution (22) (PDB entry 1SVB) was used as the
basis for all depictions of protein E and models of mutants. The
software program Insight II, version 95.0 (Biosym/MSI, San Diego,
Calif), was used for protein structure graphics and the Homology module
of this program was used for modeling loops and side chain rotamers.
 |
RESULTS |
Mutagenesis of the upper-lateral surface of protein E.
The
amino acid residues 308, 309, 310, and 311 of the TBE virus protein E
were selected for our study. These four amino acids form an extended
loop of the upper-lateral surface of protein E. The topography of this
site on the protein E dimer and a detailed view of our region of
interest are shown in Fig. 1. A striking structural feature of this area is its high content of charged amino
acid side chains. In particular, the negatively charged residue 308 (Asp) and the positively charged residue 311 (Lys) are in close
proximity, enabling the formation of a salt bridge between these two
residues (22). The polar, but uncharged side chain of
residue 310 (Thr) protrudes below this salt bridge, whereas the side
chain of Lys 309 is located on the other side of Asp 308, but is too
far away to intimately interact with its neighbor. Comparison of
various flavivirus sequences reveals that Lys 309 is conserved among
all tick-borne flaviviruses, but this residue is absent from the
mosquito-borne flavivirus sequences (22).

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FIG. 1.
Topography of Asp 308, Lys 309, Thr 310, and Lys 311 on
the TBE virus E protein. (A) Top view (upper) and side view (lower) of
the ectodomain region of the E dimer (22) with the main
chain shown as a ribbon. Blue, domains I and II; red, domain III;
yellow, residues 308 to 311. The carboxy terminus of each subunit,
which in the full-length E protein is contiguous with the stem-anchor
region, is indicated by a "C". (B) Enlarged image of domain III as
viewed from the direction of the arrows in panel A. The carbons and
side chains of each residue are shown with the hydrogen atoms omitted.
Amino acids 308 to 311 are shown as ball-and-stick forms; the others
are shown as lines. Atom colors: green, carbon; blue, nitrogen; red,
oxygen; yellow, sulfur. The N and C termini of domain III (residues 301 and 395, respectively) are indicated.
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We constructed TBE virus mutants that carried single point mutations at
each of the four positions 308 to 311, mutants that
carried
combinations of two of these mutations, and mutants with
a single
protein E mutation coupled with a specific deletion in
the 3'-NCR
(
16). All mutants generated in this study are listed
in
Table
2 and were analyzed according to
exactly the same experimental
scheme. For clarity, results are
summarized for each mutant or
set of related mutants and presented in
separate sections below.
Amino acid Lys 309.
Two different mutations were introduced at
this position. First, since Lys 309 is present in all tick-borne
flavivirus sequences but absent from the mosquito-borne flaviviruses,
this residue was deleted. In a second construct, Lys 309 was replaced
by a Leu residue, a nonpolar uncharged residue of similar size. We anticipated that this mutation would be more likely to yield viable virus than the deletion mutation but would still be useful for clarifying the functional importance of the positive charge at position
309. Indeed, the corresponding mutant virus, designated E(K309L), was
readily obtained from transfected BHK-21 cells, whereas in the case of
the clone carrying the deletion mutation, we recovered virus in only
one of three independently performed experiments. Nevertheless,
sufficiently high-titer virus stocks of both mutant viruses could be
prepared from infected suckling baby mouse brains (Table 2), and these
were subjected to sequence analysis of the genomic protein E coding
region. This confirmed the presence of the engineered mutations for
both mutants, but in the case of the position 309 deletion mutant an
additional mutation (Phe 332 to Tyr) was found [E(
309/F332Y); Table
2]. Inspection of the atomic structure suggests a causal link between the engineered deletion and the emergence of the secondary mutation. As
shown in Fig. 2, residue 332 is located
immediately behind residue 309. The additional hydroxyl group gained by
the Phe-to-Tyr substitution may help to fill the gap created by the
deletion and thus be able to structurally compensate for this mutation. It is likely that the deletion caused a displacement of the main chain,
because in the wild-type structure a Tyr at position 332 would collide
with the main chain amino group of residue 308 (Fig. 2).

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FIG. 2.
Spatial relationship between residues 308 to 311 and
residue 332. The view is a zoom of the annotated portion of Fig. 1B.
(A) Wild-type, showing Phe 332 as a ball-and-stick representation. The
portion of the ribbon corresponding to Lys 309 is colored light blue.
(B) Model representing mutant E( 309/F332Y), with Lys 309 deleted and
a compensating Phe-to-Tyr mutation at position 332.
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To our surprise, the biological characterization of the two amino acid
309 mutants did not reveal any significant differences
compared to the
wild-type strain Neudoerfl. They both exhibited
normal plaque
morphologies on PS cells, and plaque assays performed
at an elevated
temperature (40°C) did not provide any evidence
for temperature
sensitivity with respect to infectivity titers
or plaque morphologies
(Table
2). Similarly, quantitative growth
curves determined on CE cells
infected at an MOI of 1 revealed
no differences in the cell culture
growth capacities of these
mutants compared to the wild-type virus.
Figure
3 compares the
amount of
infectious virus released at two selected time points,
one during the
early phase of infection (12 h postinfection [p.i.])
and the other
one within the plateau phase of virus release (21
h p.i.). In the adult
mouse model (Fig.
4), both mutants proved
to be almost as virulent (as measured by the LD
50) and
infectious
(as determined by the ID
50) as the wild-type
control virus. In
order to check for genetic stability during infection
of the adult
mouse, viral RNA from the brains of two mice killed by
each mutant
was sequenced over the protein E coding region. No sequence
reversions
or additional mutations were detected in these cases.

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FIG. 3.
Growth capacities of wild-type (strain Neudoerfl) and
mutant TBE viruses on primary CE cells infected with an MOI of 1. The
values plotted were derived from duplicate experiments. The amount of
infectious virus released into the cell culture supernatant during a
1-h time period was determined 12 h p.i. (upper panel) and 21 h p.i. (lower panel).
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FIG. 4.
Virulence and infectivity of wild-type (strain
Neudoerfl) and mutant TBE viruses tested by subcutaneous inoculation of
5-week-old mice. LD50 (top panel) and ID50
(middle panel) values were determined as described in Materials and
Methods. The attenuation index (bottom panel) was calculated as the
LD50/ID50 ratio.
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Amino acids Asp 308 and Lys 311.
These two charged residues
form a salt bridge and this interaction may be important for the
structural integrity and functionality of this protein domain. To test
this hypothesis, we designed mutations that would reverse the charge
polarity of one of the partners of the salt bridge (Asp 308 to Lys, and
Lys 311 to Glu, respectively) and therefore eliminate this structure.
In addition, we constructed a double mutant containing both of these
mutations, which would potentially allow the formation of a salt bridge
in the inverted orientation. Infectious virus was readily obtained from
all three constructs, and virus stocks with high infectivity titers
were prepared (Table 2). In the cases of mutant viruses E(K311E) and E(D308K/K311E), sequencing confirmed the desired mutations and revealed
no additional mutations in the E gene. In the case of the single point
mutation at amino acid 308, however, the Lys substitution was unstable
and spontaneously changed to a Glu after two passages in baby mouse
brain (Table 2). The desired Lys mutation was still present after the
first baby mouse passage, but a second passage of this virus in either
baby mice or adult mice again selected for a Glu residue at position
308 (data not shown). A back-mutation from Lys to the original Asp
sequence would have required two separate nucleotide changes, whereas
only a single base change was necessary to produce a codon for Glu
which, like Asp, has a negative charge. In accordance with the mutation
that was actually present, this mutant was designated E(D308E).
The biological characterizations of mutants E(D308E) and E(K311E)
revealed wild-type plaque morphologies and no temperature
sensitivity
(Table
2). The growth behavior of these two mutants
on CE cells was
also indistinguishable from the wild-type virus
(Fig.
3). The double
mutant E(D308K/K311E), however, exhibited
altered plaque morphologies
at both incubation temperatures (Table
2). Moreover, there was an
approximately 10-fold reduction in
the amount of infectious virus in
the supernatant of CE cells
during the plateau phase of infection with
this mutant (Fig.
3).
The double mutant also exhibited the most distinguishing phenotype in
the adult mouse model (Fig.
4). It was found to be >1,000-fold
less
virulent than the wild type (its LD
50 was 10
4
PFU compared to <10 PFU for wild-type virus). However, its overall
infectivity (ID
50) upon peripheral subcutaneous inoculation
was
also somewhat reduced compared to the wild type. We used the
LD
50/ID
50 ratio, which we refer to as the
attenuation index, to correct
for differences in the ID
50
in order to reveal the degree to which
neuroinvasiveness itself, rather
than the overall infectivity,
was reduced. We found that the
attenuation index for the double
mutant was about 100-fold higher than
that of the wild-type
virus.
Unexpectedly, mutant E(D308E), although differing from the wild-type by
only a conservative mutation, exhibited a distinct
phenotype in the
mouse model. Both the LD
50 and the ID
50 were
found to be elevated to a similar degree, and therefore the attenuation
index was not significantly changed. Thus, the main effect of
this
mutation apparently was a reduction of peripheral infectivity
rather
than neuroinvasiveness itself. In contrast, mutation of
residue E311
had little effect on the virulence and infectivity
of TBE virus, as
demonstrated by mutant E(K311E), which exhibited
normal
LD
50 and ID
50 values. Genetic alterations
during infection
of the adult mouse were not observed for these three
mutants.
Amino acid Thr 310.
Amino acid Thr 310 is a polar but
uncharged residue embedded in an environment that carries a high
density of charged amino acids. Changing this residue into a Lys would
add an additional positive charge to this region and thus have a major
effect on its surface properties. This was found to have profound
consequences on the biological properties of the virus, and it showed
an altered phenotype in almost all of the parameters tested in this study.
The infectivity titer achieved for the virus stock of mutant E(T310K)
was higher (5 × 10
9 PFU/ml) than for all of the other
viruses, including the wild-type
parent strain. It exhibited a small,
clear plaque phenotype at
37°C and small, turbid plaques at the
elevated temperature (Table
2). On CE cells (Fig.
3), significantly
more infectious particles
of this mutant were released into the
supernatant during the early
time period (12 h p.i.) than for any of
the other mutants or wild-type
virus. The maximum value of virus
release as measured in the plateau
phase (21 h p.i.) was only slightly
higher than that of the wild
type.
In the adult mouse model (Fig.
4), E(T310K) was found to be
strongly attenuated: the LD
50 was more than 10,000-fold
higher
than the wild-type level. Although the infectivity of this
mutant
was also impaired by a factor of approximately 100, it still
achieved
a higher attenuation index than mutant E(D308K/K311E).
The protein E coding sequences of virus isolated from the brains of two
mice killed by the infection were checked to assess
the genetic
stability of the mutations during the journey of the
virus from the
peripheral inoculation site to the brain. In the
case of E(T310K),
virus isolated from one of the two mice exhibited
two novel mutations
(Table
2). (i) Nucleotide 1859 was changed
from A to G, causing a
conservative amino acid change at position
E296 from Lys to Arg. (ii)
Nucleotide 1903 was changed from A
to G, causing a change of amino acid
E311 from Lys to Glu. Significantly,
this second mutation is at a
position adjacent to the engineered
mutation at position 310 (Thr to
Lys).
Amino acid 310 (Thr to Lys) in combination with amino acid 311 (Lys
to Glu).
To test whether the above described mutation at position
311, which had emerged during infection of one of the adult mice with
mutant E(T310K), was responsible for the phenotypic reversion of this
mutant, the corresponding mutations (Thr 310 to Lys and Lys 311 to Glu)
were engineered into the infectious cDNA clone and mutant
E(T310K/K311E) was generated. Sequence analysis of the stock virus from
baby mouse brain demonstrated that this combination of mutations is
genetically stable.
The biological analysis of E(T310K/K311E) indicated that the biological
effects caused by the E310 Thr-to-Lys mutation were
at least in part
reversed by the second mutation at the neighboring
location. With
respect to the infectivity titer of the virus stock,
its plaque
morphology (Table
2), and its cell culture growth
properties (Fig.
3),
mutant E(T310K/K311E) was indistinguishable
from the wild type, whereas
mutant E(T310K) had been shown to
be different in all of these
parameters. With respect to virulence
in the adult mouse model (Fig.
4)
mutant E(T310K/K311E) exhibited
LD
50 and ID
50
values that were between those observed for wild-type
virus and mutant
E(T310K) but had an almost wild-type level attenuation
index. Thus, we
conclude that mutant E(T310K/K311E) more closely
resembled the virulent
wild-type virus rather than the single-amino-acid
mutant E(T310K), with
the exception that it exhibited an impaired
peripheral infectivity
compared to wild-type
virus.
Amino acid 310 (Thr to Lys) in combination with deletions in the
3'-NCR.
Of the protein E mutants analyzed, the most significant
attenuation had been obtained by the mutation of 310 Thr to Lys.
Previously, we observed that certain deletions in the 3'-NCRs of TBE
virus also caused significant attenuation while maintaining good
peripheral infectivity (16). To test whether these two
attenuating principles could be combined in an additive or even
cooperative manner, we designed two mutants that contained both the Thr
310-to-Lys mutation and one of two different 3'-NCR deletions that had
been studied previously (Table 2). Sequence analysis of the protein E
coding regions and the 3'-NCRs of the derived viral mutants confirmed the presence of the desired changes, but no additional mutations were
detected. The infectivity titer of the E(T310K)3'(
10847) mutant was somewhat lower than for the other mutants. Both mutants exhibited a small-plaque phenotype and turbid plaques at the elevated temperature, similar to mutant E(T310K), which contains the same protein E mutation but a wild-type 3'-NCR. For mutant
E(T310K)3'(
10919) plaques were turbid already at the standard
incubation temperature (Table 2). In contrast to E(T310K), both mutants
released only wild-type levels of infectious virus into the supernatant
of infected CE cells at 12 h p.i. and significantly lower levels
at 21 h p.i. (Fig. 3).
In the adult mouse model (Fig.
4), both mutants that combined mutation
Thr 310 to Lys with 3'-NCR deletions were found to
be almost
completely apathogenic. In the case of mutant E(T310K)3'(

10847),
not
a single mouse was killed at any inoculation dose. In the
case of
mutant E(T310K)3'(

10919), one mouse was killed at the
highest inoculation dose (10
6 PFU). However, the
combination of these two attenuating principles
also strongly impaired
the peripheral infectivity of these two
mutants, as demonstrated by the
elevated ID
50 values. Due to the
inability to achieve even
higher inoculation doses, it was not
possible to calculate true
LD
50 values for these two mutants.
The LD
50 and
the derived LD
50/ID
50 attenuation index values
shown
in the figure thus represent the lowest possible estimates
calculated
under the assumption that an inoculation dose of
10
7 PFU would have killed all of the mice. It seems fair to
assume,
however, that the real values would turn out to be
significantly
higher than those shown in the
figure.
Both of these highly attenuated combination mutants induced a solid
protective immunity. We observed that every animal that
had
seroconverted (and this was the parameter on which the ID
50 calculations were based) was completely protected against a subsequent
challenge with a 100-fold lethal dose of virulent TBE virus (data
not
shown).
 |
DISCUSSION |
There is considerable evidence that the upper lateral surface of
the flavivirus protein E is part of an important functional determinant. Indirect evidence for this assumption has been derived from the molecular structure of the TBE virus protein E, as well as
from studies on various flavivirus mutants. Recognition of a
still-unidentified flavivirus cell surface receptor is the most likely
function associated with this region. Some mosquito-borne flaviviruses
contain an RGD sequence motif at a position corresponding to a
four-amino-acid insert between amino acids 386 and 387 in the TBE
sequence (22). RGD motifs are known to mediate the binding of cellular or viral proteins to members of the integrin protein family
(25). However, a recent mutagenesis study of YF virus strain
17D demonstrated that integrins do not function as major receptors for
this virus (28). The four-amino-acid insert of mosquito-borne flaviviruses probably forms a loop that may cover or at
least interact with the upper lateral surface region that was
investigated for TBE virus in this study. This region is also part of
one of the two potential heparan sulfate binding sites that have been
described for dengue type 2 virus (2). The data presented in
this study demonstrate, however, that none of the four investigated
amino acid residues are absolutely essential for the specific
recognition of a receptor, because substitutions at each of the four
positions yielded viable virus. The lack of a rigid requirement for
particular amino acid interactions suggests that this region is not the
only determinant of virus attachment.
For the purpose of this discussion, we have constructed simplified
models of the upper-lateral surface (Fig.
5). In reality, the mutations would
probably also induce conformation alterations of the main chain, making
the pictures more complex. The results obtained by our approach suggest
a prominent functional role of residue Thr 310. Changing this residue
into a positively charged and much bulkier Lys residue (Fig. 5C) had
clear effects on the biology of TBE virus: the virus grew faster and to
high titers in tissue culture and in baby mouse brain but exhibited a
small-plaque phenotype. Its neuroinvasiveness after the peripheral
inoculation of adult mice was significantly reduced. These observations
are compatible with the idea that changing residue 310 to Lys affects the affinity of virus for certain cell surfaces in a way that accelerates virus production but simultaneously impedes virus spread
from cell to cell. A mutation of position 310 from Ser to Pro had
previously been identified in a neutralization escape mutant of Louping
ill (LI) virus, a closely related tick-borne flavivirus. This mutant
was reported to show partially reduced virulence but exhibited a
wild-type plaque morphology (9). We show here that the
effects of the mutation of Thr 310 to Lys could, to a large extent, be
reversed by a secondary mutation of Lys 311 to Glu, indicating that
there is not an absolute requirement for Thr per se in this position.
This mutation was also observed to arise spontaneously during infection
of an adult mouse. It is possible that this second mutation simply
neutralized the additional positive charge introduced by the first
mutation. Alternatively, as shown in Fig. 5D, this second mutation
might serve to bring Lys 310 into a different position through its
charge attraction and thus possibly alleviate steric hindrance of
receptor binding caused by the bulky Lys residue. Interestingly, a
mutation of YF virus Lys 303 to Gln (which by sequence alignment is
shown to be equivalent to TBE residue 311) was found to be responsible for a strongly increased virulence in a mutant strain isolated from a
vaccine-associated fatal human infection (8).

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|
FIG. 5.
Proposed interactions of charged side chains in mutants
of TBE virus. The view is a zoom of Fig 1B (see Fig. 1 legend for
details). Charge interactions between the side chains are indicated by
"+" and " " symbols. (A) Wild type, showing the salt bridge
between Asp 308 and Lys 311.(B) Mutant E(D308K/K311E), showing a
hypothetical salt bridge in reversed orientation. (C) Mutant E(T310K),
with a Thr-to-Lys substitution at position 310. (D) Mutant
E(T310K/K311E), showing a potential reorientation of the side chains at
positions 310 and 308 due to an additional Lys-to-Glu substitution at
position 311.
|
|
The X-ray crystal structure of protein E shows that residues Asp 308 and Lys 311 interact to form a salt bridge (Fig. 5A). Our observation
that the Asp 308-to-Lys mutation spontaneously reverted to a negatively
charged Glu residue demonstrates the structural importance of this
interaction. This view is further corroborated by the fact that
changing Asp 308 to Lys in combination with Lys 311 to Glu yielded a
genetically stable mutant without a tendency for back-mutation at
position 308. As shown in Fig. 5B, this double mutant can be imagined
to form a salt bridge in a reversed orientation compared to the wild
type. On the other hand, changing the charge on the other side of the
salt bridge mutating Lys 311 to Glu yielded a genetically stable,
virulent, and highly infectious virus. Clearly, this mutation also
eliminates the 308-311 salt bridge, but this was apparently tolerated
by the virus. It was reported previously that mutations at position 308 strongly impaired the neurovirulence of the closely related LI virus
(3, 9). Our data only partially support this observation. In
the adult mouse model, mutant E(D308E) was shown to have impaired infectivity but a wild-type attenuation index
(LD50/ID50 ratio). The double mutant
E(D308H/K311E) was found to be attenuated for virulence but also
impaired with respect to peripheral infectivity and cell culture growth
parameters. Moreover, this mutant exhibited heterogeneous plaque
morphologies (Table 2) and a peculiar nonlinear dose-response
relationship at intermediate inoculation doses in the adult mouse model
(not shown). In two independent experiments we observed lower survival
and infection rates at a lower inoculation dose than at the next higher
one (data not shown). At this time we cannot explain this phenomenon,
which has not been observed for any of the other mutants investigated
in this or previous studies.
The fact that only minor effects were observed after the
mutagenesis of Lys 309 came as a surprise. This large and
positively charged residue is conserved among all tick-borne
flaviviruses but is lacking in mosquito-borne flaviviruses, suggesting
an important functionality within the tick-borne group. Changing this
residue into a nonpolar Leu had hardly any effect in our test systems. Deletion of Lys 309 at first seemed to be deleterious, but a
spontaneously arising second-site mutation (Phe 332 to Tyr; Fig. 2) was
apparently able to compensate structurally for this defect, resulting
in a mutant virus with an almost wild-type phenotype. Inspection of
mosquito-borne flavivirus sequences reveals that several of them also
have a Tyr residue in the position corresponding to Phe 332 in TBE
virus. From our experiments one can conclude that Lys 309 is not
crucial for function in cell culture and mice.
Of the mutations described in this study, position 310 clearly
represents the most promising starting point for the rational design of
novel attenuated flavivirus vaccines. However, our data also
demonstrate some potential limitations of this approach: the achieved
attenuation was accompanied by an unfavorable reduction of peripheral
infectivity and the spontaneous appearance of a second-site mutation.
This illustrates how easily the virus can compensate for a single point
mutation and revert to a more virulent phenotype in an unpredictable
manner. In comparison, the attenuation indices achieved by previously
described mutants carrying deletions in the 3'-NCR were more than 10 times better than that observed for mutant E(T310K) in this study
(16). Moreover, no phenotypic reversions were observed for
the deletion mutants, and one may reason that mutations that are able
to compensate for large deletions are less likely to emerge than
second-site phenotypic suppression of single point mutations. Thus, the
3'-NCR deletions appear to be more promising in terms of both safety
and maintaining sufficient peripheral infectivity. For optimal
attenuation and vaccine safety it is reasonable to develop virus
mutants that combine different attenuating principles. The two 3'-NCR
deletion and Lys 310 combination mutants described in this study in
fact turned out to be virtually apathogenic. However, the significant
increase of the LD50 that was achieved by combining these
mutations was accompanied by a severe reduction in peripheral
infectivity. Both mutants also exhibited a restricted cell culture
growth and, with regard to vaccine development, these mutants
might already have to be considered "overattenuated," although the
seroconversion induced by these mutants still conferred a solid
protective immunity. To achieve stable and sufficient attenuation by
simultaneously retaining good growth properties and a high peripheral
infectivity, it will probably be necessary to test various combinations
of attenuating mutations and carry out an elaborate "fine-tuning"
of their biological effects. The mutants constructed and characterized
in this study provide relevant information for this ongoing process. In
addition, they may be helpful in the future for studying the
interaction of TBE virus with the cell surface during viral entry.
 |
ACKNOWLEDGMENTS |
We gratefully acknowledge the excellent technical assistance of
Heide Dippe, Jutta Ertl, Silvia Röhnke, and Melby Wilfinger.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Institute of
Virology, University of Vienna, Kinderspitalgasse 15, A-1095
Vienna, Austria. Phone: 43-1-404-90, ext. 79502. Fax:
43-1-406-21-61. E-mail:
christian.mandl{at}univie.ac.at.
 |
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